## `summarise()` has grouped output by 'patient', 'age_at_sample_exact', 'age_at_sample', 'DOB', 'DATE_OF_DIAGNOSIS'. You can override using the `.groups` argument.
## Joining, by = "PDID"
| patient | ID | age_at_sample_exact | cell_type | phase | BaitLabel | |
|---|---|---|---|---|---|---|
| 3 | PD6629 | PD6629dc | 55.05270 | PB whole | Recapture | PD6629dc |
| 4 | PD6629 | PD6629dd | 58.83094 | PB Gran | Recapture | PD6629dd |
| 1 | PD6629 | COLONY60 | 60.26831 | BFU-E-Colony | Colony | NA |
| 5 | PD6629 | PD6629de | 60.26831 | PB Gran | Recapture | PD6629de |
| 2 | PD6629 | COLONY62 | 62.28063 | BFU-E-Colony | Colony | NA |
| 6 | PD6629 | PD6629df | 63.41136 | PB Gran | Recapture | PD6629df |
| 7 | PD6629 | PD6629dg | 64.73374 | PB Gran | Recapture | PD6629dg |
| 8 | PD6629 | PD6629dh | 65.86448 | PB Gran | Recapture | PD6629dh |
tree=plot_basic_tree(PD$pdx,label = PD$patient,style="classic")
The nodes in this plot can be cross-referenced with nodes specified in subsequent results. The plot also serves to give an idea of what the topology at the top of the tree looks like.
tree=plot_basic_tree(expand_short_branches(PD$pdx,prop = 0.1),label = PD$patient,style="classic")
node_labels(tree)
Note that the different colours on the tree indicate the separately fitted mutation rate clades.
##
## Random-Effects Model (k = 1; tau^2 estimator: REML)
##
## logLik deviance AIC BIC AICc
## 0.0000 -0.0000 4.0000 -Inf 16.0000
##
## tau^2 (estimated amount of total heterogeneity): 0
## tau (square root of estimated tau^2 value): 0
## I^2 (total heterogeneity / total variability): 0.00%
## H^2 (total variability / sampling variability): 1.00
##
## Test for Heterogeneity:
## Q(df = 0) = 0.0000, p-val = 1.0000
##
## Model Results:
##
## estimate se zval pval ci.lb ci.ub
## 17.8576 1.0236 17.4466 <.0001 15.8514 19.8637 ***
##
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
| node | driver | status | child_count | type | colony_count | mean_lambda_rescaled | correction | sd_rescaled | lb_rescaled | ub_rescaled | median_rescaled | p_lt_wt |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| -1 | WT | 1 | -1 | local | 1 | 17.85758 | 1.014746 | 1.0476692 | 15.918788 | 19.99907 | 17.82518 | NA |
| 63 | DNMT3A | 1 | 56 | local | 21 | 18.29717 | 1.014746 | 0.3236644 | 17.686498 | 18.95402 | 18.28683 | 0.346950 |
| 68 | JAK2:DNMT3A | 1 | 35 | local | 25 | 18.07328 | 1.014746 | 0.5992949 | 16.962819 | 19.31095 | 18.05629 | 0.426150 |
| 59 | DNMT3A | 0 | 1 | local | 1 | 20.30765 | 1.014746 | 2.8738357 | 14.401820 | 26.71867 | 20.04911 | 0.196000 |
| 58 | CBL | 0 | 1 | local | 1 | 14.78254 | 1.014746 | 2.6064727 | 9.282933 | 20.53121 | 14.90475 | 0.883925 |
| 88 | 9pUPD:JAK2:DNMT3A | 0 | 2 | local | 2 | 19.01943 | 1.014746 | 1.3174011 | 16.620660 | 21.84153 | 18.94668 | 0.250200 |
| 76 | TET2:JAK2:DNMT3A | 1 | 8 | local | 8 | 17.20549 | 1.014746 | 0.9877071 | 15.345362 | 19.23166 | 17.17896 | 0.670825 |
All ages are in terms of post conception years. The vertical red lines denote when colonies were sampled and blue lines when targeted follow up samples were taken.
| patient | node | driver | child_count | lower_median | upper_median | lower_lb95 | lower_ub95 | upper_lb95 | upper_ub95 | N | group | age_at_diagnosis_pcy | max_age_at_sample | min_age_at_sample |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PD6629 | 63 | DNMT3A | 56 | 0.0087466 | 7.263952 | 0.0061894 | 0.0222232 | 5.937797 | 8.782189 | 8 | DNMT3A | 54.8063 | 66.59274 | 55.78097 |
| PD6629 | 68 | JAK2 | 35 | 14.2541270 | 29.728295 | 12.6154093 | 15.9897441 | 27.776801 | 31.722219 | 8 | JAK2 | 54.8063 | 66.59274 | 55.78097 |
| PD6629 | 76 | TET2 | 8 | 36.1591058 | 46.033123 | 34.3227129 | 37.9689969 | 44.237803 | 47.683728 | 8 | TET2 | 54.8063 | 66.59274 | 55.78097 |
| PD6629 | 88 | 9pUPD | 2 | 32.8006950 | 46.316776 | 30.8979890 | 34.6854530 | 44.430877 | 48.241853 | 8 | 9pUPD | 54.8063 | 66.59274 | 55.78097 |
## Timings using the Clade Specific Rates
| label | node | het.sensitivity | chr | start | end | nhet | nhom | mean_loh_event | lower_loh_event | upper_loh_event | t_before_end | t_before_end_lower | t_before_end_upper | kb | count_in_bin | count_se | pmut | pmut_se | xmean | xse_mean | xsd | x2.5. | x50. | x97.5. | xn_eff | xRhat | lmean | lse_mean | patient | driver3 | child_count |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LOH_9pUPD | 88 | 0.9103 | 9 | 14690 | 33393006 | 0 | 2 | 43.59 | 37.76 | 46.24 | 2.736 | 0.08701 | 8.561 | 33300000 | 6654 | 81.57 | 0.01453 | 0.0001782 | 0.7977 | 0.001115 | 0.17 | 0.367 | 0.8425 | 0.9936 | 23273 | 1 | 3.42 | 0.0003039 | PD6629 | 9pUPD:JAK2:DNMT3A | 2 |
Here we exclude all local CNAs and depict as color VAF plots